Locus 2085

Sequence ID 3L_DroMel_CAF1
Location 5,736,759 – 5,736,964
Length 205
Max. P 0.909586
window3248 window3249 window3250

overview

Window 8

Location 5,736,759 – 5,736,857
Length 98
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 69.46
Mean single sequence MFE -16.48
Consensus MFE -13.15
Energy contribution -13.15
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.67
Structure conservation index 0.80
SVM decision value 0.73
SVM RNA-class probability 0.835262
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5736759 98 - 23771897
UCAGCAGUUGCCUCAGUGUGGCCUCUGUCUGAACAUGGCACUGUCACAAUCGUAUCCAAUCUAUUAACCUGUUUUCUUAUACUUAUUAAAGU--------UAAUUU-
(((((((..(((.......)))..))).))))...((((...))))..............................................--------......- ( -14.00)
>DroSec_CAF1 6591 106 - 1
UCAGCAGUUGCCUCAGUGUGGCCUCUGUCUGAACAUGGCACUGUCACAAUCGUGUCCAAUCUAUUAAUCUGUUUUCCUAUACUUAUUAAAGUAAAUGCAUUAAUUA-
(((((((..(((.......)))..))).))))...((((((..........))).))).....................(((((....))))).............- ( -20.10)
>DroSim_CAF1 6590 106 - 1
UCAGCAGUUGCCUCAGUGUGGCCUCUGUCUGAACAUGGCACUGUCACAAUCGUGUCCAAUCUAUUAACCUGUUUUCCUAUACUUAUUAAAGUAAAUGCAUUAAUUA-
(((((((..(((.......)))..))).))))...((((((..........))).))).....................(((((....))))).............- ( -20.10)
>DroEre_CAF1 6546 86 - 1
UCAGCAGUUGCCUCUGUGUGGCCUCUGUCUGAACAUGGCACUGUCACAAUUCAAUCCA-CCUAUCAACCAAAUUUCACA--------------------UAAAGUAU
(((((((..(((.......)))..))).))))...((((...))))............-....................--------------------........ ( -14.00)
>DroYak_CAF1 6595 81 - 1
UCAGCAGUUGCCUUAGUGUGGCCUCUGUCUGAACAUGGCACUGUCACAAUUGAAACCA-CCUAUCUA----UUUAUGCA--------------------UUAAUUA-
(((((((..(((.......)))..))).))))...(((.....(((....)))..)))-........----........--------------------.......- ( -14.80)
>DroAna_CAF1 6737 78 - 1
UCAGCAGUUGCCGUUCUGUGGCCUCUGUCUGAACAUGCCACUGCUACAGU---AUACUUUAAAUGAAUCUUCCUUCCGCCA--------------------------
..((((((.((.((((...(((....))).))))..)).)))))).....---............................-------------------------- ( -15.90)
>consensus
UCAGCAGUUGCCUCAGUGUGGCCUCUGUCUGAACAUGGCACUGUCACAAUCGUAUCCAAUCUAUUAACCUGUUUUCCUAUA__________________UUAAUUA_
(((((((..(((.......)))..))).))))........................................................................... (-13.15 = -13.15 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,736,789 – 5,736,893
Length 104
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.43
Mean single sequence MFE -26.31
Consensus MFE -24.10
Energy contribution -23.93
Covariance contribution -0.17
Combinations/Pair 1.15
Mean z-score -1.80
Structure conservation index 0.92
SVM decision value 1.07
SVM RNA-class probability 0.909586
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5736789 104 - 23771897
ACAUUUUGCCAGAACAAAUUCC---AGGCAUUGUCGUCUUCAGCAGUUGCCUCAGUG--UGGCCUCUGUCUGAACAUGGCACUGUCACAAUCGUAUCCAAUCUAUUA--AC
......................---.((((.((((((.((((((((..(((......--.)))..))).))))).)))))).)))).....................--.. ( -27.40)
>DroSec_CAF1 6629 104 - 1
ACAUUUUGCCAGAACAAAUCCC---AGGCAUUGUCGUCUUCAGCAGUUGCCUCAGUG--UGGCCUCUGUCUGAACAUGGCACUGUCACAAUCGUGUCCAAUCUAUUA--AU
...........(.(((......---.((((.((((((.((((((((..(((......--.)))..))).))))).)))))).)))).......))).).........--.. ( -28.14)
>DroEre_CAF1 6565 103 - 1
ACAUUUUGCCAGAACAAAUCUC---AGGCUUUGACGUCUUCAGCAGUUGCCUCUGUG--UGGCCUCUGUCUGAACAUGGCACUGUCACAAUUCAAUCCA-CCUAUCA--AC
......(((((...........---((((......))))(((((((..(((......--.)))..))).))))...)))))..................-.......--.. ( -22.60)
>DroYak_CAF1 6610 102 - 1
ACAUUUUGCCAGAACAAAUCCC---AGGCUUUGACGUCUUCAGCAGUUGCCUUAGUG--UGGCCUCUGUCUGAACAUGGCACUGUCACAAUUGAAACCA-CCUAUCU--A-
......(((((...((((.(..---..).)))).....((((((((..(((......--.)))..))).)))))..)))))..................-.......--.- ( -22.80)
>DroMoj_CAF1 6854 110 - 1
ACAUUUUGCUAGAAUAAAGCUCCAAAGGCUUUGGCGUCUUCAGCAGUUGCCUCAUUUCAUGGCCUCGGUCUGAACAUGCCAUUGCUACAAAAGUUCCUAUA-UAUUCCCAG
...(((((.(((...((((((.....))))))(((((.((((((.(..(((.........)))..).).))))).)))))....)))))))).........-......... ( -26.60)
>DroAna_CAF1 6750 101 - 1
ACAUUCUGCCAGACCAAAGCCC---AGGCAUUGGCGUCUUCAGCAGUUGCCGUUCUG--UGGCCUCUGUCUGAACAUGCCACUGCUACAGU---AUACUUUAAAUGA--AU
......................---.((((.((((((.((((((((..((((.....--))))..))).))))).)))))).)))).....---.............--.. ( -30.30)
>consensus
ACAUUUUGCCAGAACAAAUCCC___AGGCAUUGACGUCUUCAGCAGUUGCCUCAGUG__UGGCCUCUGUCUGAACAUGGCACUGUCACAAUCGUAUCCA_UCUAUUA__AC
..........................(((..((((((.((((((((..(((.........)))..))).))))).))))))..)))......................... (-24.10 = -23.93 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,736,857 – 5,736,964
Length 107
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 77.90
Mean single sequence MFE -26.30
Consensus MFE -18.80
Energy contribution -19.02
Covariance contribution 0.22
Combinations/Pair 1.25
Mean z-score -0.96
Structure conservation index 0.71
SVM decision value -0.03
SVM RNA-class probability 0.520438
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5736857 107 - 23771897
AUUCCCUAUUAUGCGAG-UUGGCAGAACUUAAUUCCGGACCUGGUACACCUU--CGGGUGCUAAGUGCGGCCAGACAUUUUGCCAGAACAAAUUCC---AGGCAUUGUCGUCU
((((.(......).)))-)((((...(((((...(((....)))..((((..--..)))).)))))...))))((((...((((.(((....))).---.)))).)))).... ( -30.20)
>DroVir_CAF1 6820 107 - 1
------UAUGAUACUAGUUUUGCAAAACUUAAUUCCGGAUUUGGUAUAACUCUUGAGCUGCCAACUACGGCCAGACAUUUUGCUAGAACAAAGCUCCAAAGGCUUUGGCGUCU
------...((..((.(((((((((((.......(((...((((((...((....)).))))))...))).......)))))).)))))((((((.....))))))))..)). ( -24.54)
>DroGri_CAF1 6998 107 - 1
------UAUGAUUUGAUUUUUGCAAAACUUAAUUCCGGAUUUGGUAUAACUCUUGAGCUGCCAACUACGGCCAGACAUUUUGCUAGAGCAAAGCUCCAAAGGCUUUGGCGUCU
------...(((....((((.((((((.......(((...((((((...((....)).))))))...))).......)))))).))))(((((((.....)))))))..))). ( -22.44)
>DroEre_CAF1 6632 101 - 1
------UAAUACGCUAG-UUGGCAGAACUUAAUUCCGGAUUUGGUACACCUU--CGGGUGCUAAGUACGGCCAGACAUUUUGCCAGAACAAAUCUC---AGGCUUUGACGUCU
------...........-(((((((((.......(((.((((((..((((..--..)))))))))).))).......)))))))))..........---((((......)))) ( -27.74)
>DroYak_CAF1 6676 101 - 1
------UAUUAUGCGAG-UUGGCAGAACUUAAUUCCGGAUUUGGUACACCUU--CGGGUGCUAAGUACGGCCAGACAUUUUGCCAGAACAAAUCCC---AGGCUUUGACGUCU
------......(((..-(((((((((.......(((.((((((..((((..--..)))))))))).))).......)))))))))..((((.(..---..).)))).))).. ( -29.24)
>DroPer_CAF1 15123 92 - 1
----------------A-UUGGCAAAACUUAAUUCCGGAUUUGGUUCACCUUU-UGGCUAUCAAACACGGCCAGACAUUUUGCCAGAGCAAACCCC---AGGCCUUGGCGUCU
----------------.-(((((((((.......(((..((((((...((...-.))..))))))..))).......)))))))))..........---..((....)).... ( -23.64)
>consensus
______UAUUAUGCGAG_UUGGCAAAACUUAAUUCCGGAUUUGGUACACCUU__CGGCUGCCAAGUACGGCCAGACAUUUUGCCAGAACAAAUCCC___AGGCUUUGGCGUCU
..................(((((((((.......(((.((((((((............)))))))).))).......))))))))).............((((......)))) (-18.80 = -19.02 +   0.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:03 2006